Identification and characterization of a novel fumarase gene by metagenome expression cloning from marine microorganisms

Microbial Cell Factories

Volumn 9, Issue , 2010, Pages

  Jiang, Chengjian ^a   Wu, Lan Lan ^a   Zhao, Gao Chao ^a   Shen, Pei Hong ^a   Jin, Ke ^a   Hao, Zhen Yu ^a   Li, Shuang Xi ^a   Ma, Ge Fei ^a   Luo, Feng Feng ^a   Hu, Guo Qing ^a   Kang, Wen Long ^a   Qin, Xing Mei ^a   Bi, You Li ^a   Tang, Xian Lai ^a   Wu, Bo ^a,b  

^a GUANGXI UNIVERSITY   (China)

^b GUANGXI UNIVERSITY FOR NATIONALITIES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

FUMARATE HYDRATASE; FUMARIC ACID; MALIC ACID; RECOMBINANT PROTEIN; SEA WATER; FUMARIC ACID DERIVATIVE; MALIC ACID DERIVATIVE;

AMINO ACID SEQUENCE; ARTICLE; BACTEROIDES; BIOCATALYSIS; CATALYSIS; CONTROLLED STUDY; DNA LIBRARY; DNA SCREENING; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ISOLATION; ENZYME KINETICS; ESCHERICHIA COLI; GENE EXPRESSION; GENE IDENTIFICATION; GENE VECTOR; GENETIC TRAIT; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDRATION; MARINE SPECIES; METAGENOME; METAGENOMICS; MICROBIAL DIVERSITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PARABACTEROIDES DISTASONIS; PH; PLASMID; PROTEIN PURIFICATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TEMPERATURE; AQUATIC SPECIES; BIOLOGY; CHEMISTRY; CLASSIFICATION; ENZYMOLOGY; GENETICS; ISOLATION AND PURIFICATION; KINETICS; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE ALIGNMENT;

BACTEROIDES SP.;

AMINO ACID SEQUENCE; AQUATIC ORGANISMS; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; FUMARATE HYDRATASE; FUMARATES; KINETICS; MALATES; METAGENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; TEMPERATURE;

EID: 78549273071     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-9-91     Document Type: Article

References (36)

1. Rose IA, Weaver TM. The role of the allosteric B site in the fumarase reaction. Proc Natl Acad Sci USA 2004, 101(10):3393-3397. 10.1073/pnas.0307524101, 373472, 14990798.
2. Genda T, Watabe S, Ozaki H. Purification and characterization of fumarase from Corynebacterium glutamicum. Biosci Biotechnol Biochem 2006, 70(5):1102-1109. 10.1271/bbb.70.1102, 16717409.
3. Fukuda W, Ismail YS, Fukui T, Atomi H, Imanaka T. Characterization of an archaeal malic enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Archaea 2005, 1(5):293-301. 10.1155/2005/250757, 2685551, 15876562.
4. Pankhurst KL, Mowat CG, Miles CS, Leys D, Walkinshaw MD, Reid GA, Chapman SK. Role of His505 in the soluble fumarate reductase from Shewanella frigidimarina. Biochemistry 2002, 41(27):8551-8556. 10.1021/bi020155e, 12093271.
5. Goh LL, Barkham T, Sim TS. Molecular cloning and functional characterization of fumarases C in Neisseria species. Antonie van Leeuwenhoek 2005, 87(3):205-213. 10.1007/s10482-004-3719-4, 15803386.
6. Estevez M, Skarda J, Spencer J, Banaszak L, Weaver T. X-ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation. Protein Sci 2002, 11(6):1552-1557. 10.1110/ps.0201502, 2373640, 12021453.
7. Shimoyama T, Rajashekhara E, Ohmori D, Kosaka T, Watanabe K. MmcBC in Pelotomaculum thermopropionicum represents a novel group of prokaryotic fumarases. FEMS Microbiol Lett 2007, 270(2):207-213. 10.1111/j.1574-6968.2007.00665.x, 17319878.
8. Weiner B, Poelarends GJ, Janssen DB, Feringa BL. Biocatalytic enantioselective synthesis of N-substituted aspartic acids by aspartate ammonia lyase. Chemistry 2008, 14(32):10094-10100. 10.1002/chem.200801407, 18844200.
9. Kennedy J, Marchesi JR, Dobson AD. Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 2008, 7:27. 10.1186/1475-2859-7-27, 2538500, 18717988.
10. Sessitsch A, Hackl E, Wenzl P, Kilian A, Kostic T, Stralis-Pavese N, Sandjong BT, Bodrossy L. Diagnostic microbial microarrays in soil ecology. New Phytol 2006, 171(4):719-735. 10.1111/j.1469-8137.2006.01824.x, 16918544.
11. Tuffin M, Anderson D, Heath C, Cowan DA. Metagenomic gene discovery: how far have we moved into novel sequence space?. Biotechnol J 2009, 4(12):1671-1683. 10.1002/biot.200900235, 19946882.
12. Kennedy J, Flemer B, Jackson SA, Lejon DP, Morrissey JP, O'Gara F, Dobson AD. Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. Mar Drugs 2010, 8(3):608-628. 10.3390/md8030608, 2857354, 20411118.
13. Steele HL, Jaeger KE, Daniel R, Streit WR. Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 2009, 16(1-2):25-37. 10.1159/000142892, 18957860.
14. Singh J, Behal A, Singla N, Joshi A, Birbian N, Singh S, Bali V, Batra N. Metagenomics: Concept, methodology, ecological inference and recent advances. Biotechnol J 2009, 4(4):480-494. 10.1002/biot.200800201, 19288513.
15. Groisillier A, Hervé C, Jeudy A, Rebuffet E, Pluchon PF, Chevolot Y, Flament D, Geslin C, Morgado IM, Power D, Branno M, Moreau H, Michel G, Boyen C, Czjzek M. MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organisms. Microb Cell Fact 2010, 9:45. 10.1186/1475-2859-9-45, 2897777, 20546566.
16. Urakawa H, Martens-Habbena W, Stahl DA. High abundance of ammonia-oxidizing Archaea in coastal waters, determined using a modified DNA extraction method. Appl Environ Microbiol 2010, 76(7):2129-2135. 10.1128/AEM.02692-09, 2849251, 20118363.
17. Li G, Wang K, Liu YH. Molecular cloning and characterization of a novel pyrethroid-hydrolyzing esterase originating from the Metagenome. Microb Cell Fact 2008, 7:38. 10.1186/1475-2859-7-38, 2657102, 19116015.
18. Acevedo JP, Reyes F, Parra LP, Salazar O, Andrews BA, Asenjo JA. Cloning of complete genes for novel hydrolytic enzymes from Antarctic sea water bacteria by use of an improved genome walking technique. J Biotechnol 2008, 133(3):277-286. 10.1016/j.jbiotec.2007.10.004, 18055055.
19. Angel R, Soares MI, Ungar ED, Gillor O. Biogeography of soil archaea and bacteria along a steep precipitation gradient. ISME J 2010, 4(4):553-563. 10.1038/ismej.2009.136, 20033070.
20. Kulkarni G, Sabnis NA, Harris BG. Cloning, expression, and purification of fumarase from the parasitic nematode Ascaris sum. Protein Expr Purif 2004, 33(2):209-213. 10.1016/j.pep.2003.09.005, 14711508.
21. Mizobata T, Fujioka T, Yamasaki F, Hidaka M, Nagai J, Kawata Y. Purification and characterization of a thermostable class II fumarase from Thermus thermophilus. Arch Biochem Biophys 1998, 355(1):49-55. 10.1006/abbi.1998.0693, 9647666.
22. Lin W, Chan M, Goh LL, Sim TS. Molecular basis for thermal properties of Streptomyces thermovulgaris fumarase C hinge at hydrophilic amino acids R163, E170 and S347. Appl Microbiol Biotechnol 2007, 75(2):329-335. 10.1007/s00253-006-0822-7, 17245573.
23. Behal RH, Oliver DJ. Biochemical and molecular characterization of fumarase from plants: purification and characterization of the enzyme--cloning, sequencing, and expression of the gene. Arch Biochem Biophys 1997, 348(1):65-74. 10.1006/abbi.1997.0359, 9390175.
24. Van Kuijk BL, Van Loo ND, Arendsen AF, Hagen WR, Stams AJ. Purification and characterization of fumarase from the syntrophic propionate-oxidizing bacterium strain MPOB. Arch Microbiol 1996, 165(2):126-131. 10.1007/s002030050307, 8593099.
25. van Vugt-Lussenburg BM, van der Weel L, Hagen WR, Hagedoorn PL. Identification of two [4Fe-4S]-cluster-containing hydro-lyases from Pyrococcus furiosus. Microbiology 2009, 155(Pt 9):3015-3020. 10.1099/mic.0.030320-0, 19520720.
26. Kotik M. Novel genes retrieved from environmental DNA by polymerase chain reaction: current genome-walking techniques for future metagenome applications. J Biotechnol 2009, 144(2):75-82. 10.1016/j.jbiotec.2009.08.013, 19712711.
27. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual. 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 3.
28. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970, 227(5259):680-685. 10.1038/227680a0, 5432063.
29. Fuhrman JA, Comeau DE, Hagström A, Chan AM. Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl Environ Microbiol 1988, 54(6):1426-1429. 202673, 16347652.
30. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 2007, 24(8):1596-1599. 10.1093/molbev/msm092, 17488738.
31. Lian HZ, Mao L, Ye XL, Miao J. Simultaneous determination of oxalic, fumaric, maleic and succinic acids in tartaric and malic acids for pharmaceutical use by ion-suppression reversed-phase high performance liquid chromatography. J Pharmaceut Biomed 1999, 19(3-4):621-625.
32. Stams AJM, Kremer DR, Nicolay K, Weenk GH, Hansen TA. Pathway of propionate formation in Desulfobulbus propionicus. Arch Microbiol 1984, 139(2-3):167-173.
33. O'Hare MC, Doonan S. Purification and structural comparisons of the cytosolic and mitochondrial isoenzymes of fumarase from pig liver. Biochim Biophys Acta 1985, 827(2):127-134.
34. Jiang C, Shen P, Yan B, Wu B. Biochemical characterization of a metagenome-derived decarboxylase. Enzyme Microb Technol 2009, 45(1):58-63.
35. Sharma S, Khan FG, Qazi GN. Molecular cloning and characterization of amylase from soil metagenomic library derived from Northwestern Himalayas. Appl Microbiol Biotechnol 2010, 86(6):1821-1828. 10.1007/s00253-009-2404-y, 20054535.
36. Stanislawski J. Enzyme Kinetics, version 1.5. 1991, Trinity Software. Fort Pierce, Fla.